Read Skyline exported files

read_skyline(files)

Arguments

files

Character vector with filepaths to Skyline exported files in CSV format.

Value

LipidomicsExperiment object.

Examples

datadir <- system.file("extdata", package = "lipidr")

# all csv files
filelist <- list.files(datadir, "data.csv", full.names = TRUE)
d <- read_skyline(filelist)
#> Successfully read 3 methods.
#> Your data contain 58 samples, 10 lipid classes, 277 lipid molecules.

# View automatically generated lipid annotations
rowData(d)
#> DataFrame with 279 rows and 26 columns
#>        filename         Molecule Precursor.Mz Precursor.Charge Product.Mz
#>     <character>      <character>    <numeric>        <integer>  <numeric>
#> 1   A1_data.csv          PE 32:0        692.5                1      551.5
#> 2   A1_data.csv          PE 32:1        690.5                1      549.5
#> 3   A1_data.csv          PE 32:2        688.5                1      547.5
#> 4   A1_data.csv          PE 34:1        718.5                1      577.5
#> 5   A1_data.csv      PE 34:1 NEG        716.5                1      196.0
#> ...         ...              ...          ...              ...        ...
#> 275 F2_data.csv       PC(P-40:3)      824.600                1     184.10
#> 276 F2_data.csv       PC(P-40:4)      822.600                1     184.10
#> 277 F2_data.csv       PC(P-40:5)      820.600                1     184.10
#> 278 F2_data.csv       PC(P-40:6)      818.600                1     184.10
#> 279 F2_data.csv 15:0-18:1(d7) PC      753.615                1     184.07
#>     Product.Charge       clean_name     ambig not_matched      istd  class_stub
#>          <integer>         <factor> <logical>   <logical> <logical> <character>
#> 1                1          PE 32:0     FALSE       FALSE     FALSE          PE
#> 2                1          PE 32:1     FALSE       FALSE     FALSE          PE
#> 3                1          PE 32:2     FALSE       FALSE     FALSE          PE
#> 4                1          PE 34:1     FALSE       FALSE     FALSE          PE
#> 5                1          PE 34:1     FALSE       FALSE     FALSE          PE
#> ...            ...              ...       ...         ...       ...         ...
#> 275              1 PCP-40:3             FALSE       FALSE     FALSE         PCP
#> 276              1 PCP-40:4             FALSE       FALSE     FALSE         PCP
#> 277              1 PCP-40:5             FALSE       FALSE     FALSE         PCP
#> 278              1 PCP-40:6             FALSE       FALSE     FALSE         PCP
#> 279              1 PC 15:0-18:1(d7)     FALSE       FALSE      TRUE          PC
#>          chain1       l_1       s_1      chain2       l_2       s_2      chain3
#>     <character> <integer> <integer> <character> <integer> <integer> <character>
#> 1          32:0        32         0                    NA        NA            
#> 2          32:1        32         1                    NA        NA            
#> 3          32:2        32         2                    NA        NA            
#> 4          34:1        34         1                    NA        NA            
#> 5          34:1        34         1                    NA        NA            
#> ...         ...       ...       ...         ...       ...       ...         ...
#> 275        40:3        40         3                    NA        NA            
#> 276        40:4        40         4                    NA        NA            
#> 277        40:5        40         5                    NA        NA            
#> 278        40:6        40         6                    NA        NA            
#> 279        15:0        15         0        18:1        18         1            
#>           l_3       s_3      chain4       l_4       s_4  total_cl  total_cs
#>     <logical> <logical> <character> <logical> <logical> <integer> <integer>
#> 1          NA        NA                    NA        NA        32         0
#> 2          NA        NA                    NA        NA        32         1
#> 3          NA        NA                    NA        NA        32         2
#> 4          NA        NA                    NA        NA        34         1
#> 5          NA        NA                    NA        NA        34         1
#> ...       ...       ...         ...       ...       ...       ...       ...
#> 275        NA        NA                    NA        NA        40         3
#> 276        NA        NA                    NA        NA        40         4
#> 277        NA        NA                    NA        NA        40         5
#> 278        NA        NA                    NA        NA        40         6
#> 279        NA        NA                    NA        NA        33         1
#>           Class
#>     <character>
#> 1            PE
#> 2            PE
#> 3            PE
#> 4            PE
#> 5            PE
#> ...         ...
#> 275          PC
#> 276          PC
#> 277          PC
#> 278          PC
#> 279          PC